Pairwise sequence comparison: Hints
You will find below some hints for the EMBnet course on pairwise sequence comparison.
Pairwise alignment with LALIGN - Hints
For most of the tools used during this practical, you can use the ID or Accession instead of copy & pasting the sequence.
Make sure you specify the right input sequence format in the pull-down list (i.e. SwissProt ID or AC).
Dotplot using Dotlet - Hints
- Look at the Dotlet documentation ;-)
- The gray level of a pixel represents the score of the window of aligned residues at this position in both sequences. The gray scaleon the right allows you to adjust how the colours map onto the scores.
- Most of the time an optimal position for the grayscale is, when it extends just across the smaller "bump" in the purple score distribution.Thus noise will be masked as black and the high scores are white.
- The diagonal lines represent alignments between the two sequences. By clicking inside the dotplot you can see the position of the two sequences againsteach other.
- It's not that difficult ;-)
- When the window size is reduced, the dotplot will have more background noise, but also more details. If the window size is increased, the details are smoothed out.
- This is usefull to identify repeats in a protein (two or more parallel diagonals) and low complexity regions (fuzzy spots).